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Sample GSM3561981 Query DataSets for GSM3561981
Status Public on Feb 12, 2019
Title Male 20 min digestion SSP
Sample type SRA
Source name Male F123 mESCs from Cast/129 backgrond
Organism Mus musculus
Characteristics strain background: Cast/129
Sex: Male
cell line: F123
cell type: mES cells
Treatment protocol Nuclei are isolated and treated with a limited amount of micrococcal nuclease for a specific amount of time
Growth protocol Cells are grown under standard mESC culture conditions (15% FBS, serum + LIF, 1X Pen/Strep) on 0.1% gelatin (following two passages on mitotically inactivated MEF feeders)
Extracted molecule genomic DNA
Extraction protocol Cells are lysed using a standard phenol-choloroform-isoamyl alcohol purification
Mnase-SSP is performed using the single-stranded library prep of Gansauge and Meyer (Nature Prot. 2013)
Libraries are sequenced with a custom read 1 primer on Illumina MiSeq or NextSeq instruments
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina NextSeq 500
Description ML_20
Male F123 mESCs from Cast/129 backgrond
Data processing library strategy: Mnase-SSP
Reads were mapped to a combined Burrows-Wheeler reference of mm10 using bowtie2. They were then filtered using custom Python scripts to generate deduplicated, sorted, indexed BAM files
Genome_build: mm10
Supplementary_files_format_and_content: processed data are aligned, deduplicated, sorted, and indexed BAM files that all scripts in the associated GitHub account
Submission date Jan 14, 2019
Last update date Feb 14, 2019
Contact name Vijay Ramani
Organization name UCSF
Department Biochemistry & Biophysics
Lab Ramani Lab
Street address 600 16th St, GH-S312B
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
Platform ID GPL19057
Series (1)
GSE125053 High-resolution analysis of chromatin structure by Mnase-SSP
BioSample SAMN10741252
SRA SRX5247948

Supplementary file Size Download File type/resource
GSM3561981_ML_20_SSP.sorted.deduped.bam 2.4 Gb (ftp)(http) BAM
GSM3561981_ML_20_SSP.sorted.deduped.bam.bai.gz 1.1 Mb (ftp)(http) BAI
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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